11-22893289-C-T

Variant names:

• chr11-22893289-C-T
• rs987865
• ENST00000499625.1:n.485-27229C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000499625.1(ENSG00000246225):​n.485-27229C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 151,768 control chromosomes in the GnomAD database, including 1,769 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1769 hom., cov: 31)
• Consequence: ENSG00000246225 ENST00000499625.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 2 publications found

Genes affected

ENSG00000246225 (HGNC:):

LINC02718 (HGNC:54235): (long intergenic non-protein coding RNA 2718)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02718	NR_187205.1	n.493-27229C>T		intron_variant	Intron 3 of 13
LINC02718	NR_187206.1	n.493-27229C>T		intron_variant	Intron 3 of 11
LINC02718	NR_187207.1	n.493-27229C>T		intron_variant	Intron 3 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246225	ENST00000499625.1	n.485-27229C>T		intron_variant	Intron 3 of 4	5
ENSG00000246225	ENST00000528701.6	n.495-27229C>T		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23055 AN: 151650 Hom.: 1769 Cov.: 31

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.154

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.152 AC: 23055 AN: 151768 Hom.: 1769 Cov.: 31 AF XY: 0.153 AC XY: 11336 AN XY: 74146

African (AFR) AF: 0.147 AC: 6070 AN: 41360

American (AMR) AF: 0.109 AC: 1659 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3466

East Asian (EAS) AF: 0.197 AC: 1012 AN: 5136

South Asian (SAS) AF: 0.258 AC: 1239 AN: 4802

European-Finnish (FIN) AF: 0.124 AC: 1307 AN: 10524

Middle Eastern (MID) AF: 0.128 AC: 37 AN: 290

European-Non Finnish (NFE) AF: 0.158 AC: 10719 AN: 67924

Other (OTH) AF: 0.153 AC: 323 AN: 2108

Alfa AF: 0.157 Hom.: 244

Bravo AF: 0.145

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.65
PhyloP100		-0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs987865; hg19: chr11-22914835;